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J. Pers. Med. 2019, 9(1), 10;

VARIFI—Web-Based Automatic Variant Identification, Filtering and Annotation of Amplicon Sequencing Data

Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Dr. Bohrgasse 9, 1030 Vienna, Austria
Department of Applied Genetics und Cell Biology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
Institute of Pathology, Medical University Vienna, Währinger Gürtel 18-20, 1090 Vienna, Austria
Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, 1090 Vienna, Austria
Author to whom correspondence should be addressed.
Received: 28 December 2018 / Revised: 26 January 2019 / Accepted: 28 January 2019 / Published: 1 February 2019
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Fast and affordable benchtop sequencers are becoming more important in improving personalized medical treatment. Still, distinguishing genetic variants between healthy and diseased individuals from sequencing errors remains a challenge. Here we present VARIFI, a pipeline for finding reliable genetic variants (single nucleotide polymorphisms (SNPs) and insertions and deletions (indels)). We optimized parameters in VARIFI by analyzing more than 170 amplicon-sequenced cancer samples produced on the Personal Genome Machine (PGM). In contrast to existing pipelines, VARIFI combines different analysis methods and, based on their concordance, assigns a confidence score to each identified variant. Furthermore, VARIFI applies variant filters for biases associated with the sequencing technologies (e.g., incorrectly identified homopolymer-associated indels with Ion Torrent). VARIFI automatically extracts variant information from publicly available databases and incorporates methods for variant effect prediction. VARIFI requires little computational experience and no in-house compute power since the analyses are conducted on our server. VARIFI is a web-based tool available at View Full-Text
Keywords: personalized medicine; cancer; amplicon sequencing; variant finding; pipeline personalized medicine; cancer; amplicon sequencing; variant finding; pipeline

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Krunic, M.; Venhuizen, P.; Müllauer, L.; Kaserer, B.; von Haeseler, A. VARIFI—Web-Based Automatic Variant Identification, Filtering and Annotation of Amplicon Sequencing Data. J. Pers. Med. 2019, 9, 10.

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